A python package to download and enrich phytochemical data
This library requires wcvpy>=1.3.2, to install see https://github.com/alrichardbollans/wcvpy
To install phytochempy with pip, run:
pip install git+https://github.com/alrichardbollans/[email protected]
When using this package, please cite the appropriate data sources. These are detailed in References below.
The main methods help to retrieve organism-compound pairs from KNApSAcK and WikiData, and tidy the data by resolving plant names to the WCVP and also resolve chemical identifiers where possible.
See the notebooks in the tutorials folder for detailed examples of downloading data and calculating phytochemical diversity.
Farit Mochamad Afendi, Taketo Okada,, Mami Yamazaki, Aki-Hirai-Morita, Yukiko Nakamura, Kensuke Nakamura, Shun Ikeda, Hiroki Takahashi, Md. Altaf-Ul-Amin, Latifah, Darusman, Kazuki Saito, Shigehiko Kanaya, “KNApSAcK Family Databases: Integrated Metabolite-Plant Species Databases for Multifaceted Plant Research,” Plant Cell Physiol., 53, e1(1-12), (2012). doi: 10.1093/pcp/pcr165.
Denny Vrandečić and Markus Krötzsch, ‘Wikidata: A Free Collaborative Knowledgebase’, Communications of the ACM 57, no. 10 (2014): 78–85.
and related LOTUS initiative:
Adriano Rutz, Maria Sorokina, Jakub Galgonek, Daniel Mietchen, Egon Willighagen, Arnaud Gaudry, James G Graham, Ralf Stephan, Roderic Page, Jiří Vondrášek, Christoph Steinbeck, Guido F Pauli, Jean-Luc Wolfender, Jonathan Bisson, Pierre-Marie Allard (2022) The LOTUS initiative for open knowledge management in natural products research. eLife 11:e70780. https://doi.org/10.7554/eLife.70780
Hyun Woo Kim et al., ‘NPClassifier: A Deep Neural Network-Based Structural Classification Tool for Natural Products’, Journal of Natural Products 84, no. 11 (26 November 2021): 2795–2807, https://doi.org/10.1021/acs.jnatprod.1c00399.
GNPS Workflow:
Wang, Mingxun, Jeremy J. Carver, Vanessa V. Phelan, Laura M. Sanchez, Neha Garg, Yao Peng, Don Duy Nguyen et al. 'Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking.' Nature biotechnology 34, no. 8 (2016): 828-837.
Yannick Djoumbou Feunang et al., ‘ClassyFire: Automated Chemical Classification with a Comprehensive, Computable Taxonomy’, Journal of Cheminformatics 8, no. 1 (December 2016): 61, https://doi.org/10.1186/s13321-016-0174-y. http://classyfire.wishartlab.com
The data supplied with the package was accessed 13/12/2023.
ChEMBL Database:
Mendez D, Gaulton A, Bento AP, Chambers J, De Veij M, Félix E, Magariños MP, Mosquera JF, Mutowo P, Nowotka M, Gordillo-Marañón M, Hunter F, Junco L, Mugumbate G, Rodriguez-Lopez M, Atkinson F, Bosc N, Radoux CJ, Segura-Cabrera A, Hersey A, Leach AR. (2019) 'ChEMBL: towards direct deposition of bioassay data.' Nucleic Acids Res., 47(D1) D930-D940.
ChEMBL Web Services:
Davies M, Nowotka M, Papadatos G, Dedman N, Gaulton A, Atkinson F, Bellis L, Overington JP. (2015) 'ChEMBL web services: streamlining access to drug discovery data and utilities.' Nucleic Acids Res., 43(W1) W612-W620.
Nicolas Bosc et al., “MAIP: A Web Service for Predicting Blood‐stage Malaria Inhibitors,” Journal of Cheminformatics 13, no. 1 (December 2021): 13, https://doi.org/10.1186/s13321-021-00487-2.
CIRpy: https://github.com/mcs07/CIRpy was used to resolve given CAS Registry IDs:
CAS, ‘CAS Registry System’, Journal of Chemical Information and Computer Sciences 18, no. 1 (1978): 58–58, https://doi.org/10.1021/ci60013a609 using the NCI/CADD Chemical Identifier Resolver:https://cactus.nci.nih.gov/chemical/structure
Veber:
Daniel F. Veber et al., ‘Molecular Properties That Influence the Oral Bioavailability of Drug Candidates’, Journal of Medicinal Chemistry 45, no. 12 ( 1 June 2002): 2615–23, https://doi.org/10.1021/jm020017n.
Lipinski:
Christopher A Lipinski et al., ‘Experimental and Computational Approaches to Estimate Solubility and Permeability in Drug Discovery and Development Settings’, Advanced Drug Delivery Reviews 23, no. 1–3 (1997): 3–25.
Tool:
RDKit: Open-source cheminformatics. https://www.rdkit.org
See publication ---